Chapter 15 Rider Transposon Insertion and Phenotypic Change in Tomato Ning Jiang, Sofia Visa, Shan Wu, and Esther van der Knaap Abstract The Rider retrotransposon is ubiquitous in the tomato genome and is likely an autonomous element that still transposes to date. The majority of approxi- mately 2,000 copies of Rider are located near genes. Phenotypes associated with Rider insertion are diverse and often the result of knock out of the underlying genes. One unusual Rider-mediated phenotype resulted from a gene duplication event. By means of read-through transcription, Rider copied part of the surrounding sequence to another location in the genome, leading to high expression of one of the transposed genes, SUN, resulting in an elongated fruit shape. Transcription studies demonstrated that Rider is expressed to levels comparable to the expression of other tomato genes and that control of transposition may be regulated by antisense transcription. Taken together, Rider is a unique retrotransposon that may have played important roles in the evolution of tomato and its closest relatives. Keywords LTR Copia • Phenotype • Rider • Tomato • Transcription Abbreviations ATP Adenosine triphosphate bHLH Basic helix–loop–helix BL Blind C Cut leaf or potato leaf mutation N. Jiang Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA S. Visa Department of Mathematics and Computer Science, College of Wooster, Wooster, OH 44691, USA S. Wu • E. van der Knaap (*) Department of Horticulture and Crop Science, The Ohio State University, Wooster, OH 44691, USA e-mail:
[email protected] M.-A. Grandbastien and J.M. Casacuberta (eds.), Plant Transposable Elements, 297 Topics in Current Genetics 24, DOI 10.1007/978-3-642-31842-9_15, # Springer-Verlag Berlin Heidelberg 2012 298 N.